Biostatistics-Docker

Transcript

1. Transforming Science Through Data-driven Discovery Workshop on Bringing your favorite bioinforma<cs analysis tools to Discovery Environment using Docker Upendra Kumar DeviseAy Science Informa<cian upendra@cyverse.org @Upendra_35
3. FastQC-0.11.5
4. Let’s get started 1. Install Docker on your local machine 2. Figure out dependencies/binaries/source code 3. Create a Dockerfile, build and test the built image + 4. Submit the request for a “new tool” 6. Design UI for your app and use it •  CyVerse account (hAps://user.cyverse.org/register/) 5. Wait to hear from us
5. Terminology •  Docker image: Ready snapshot of a configured so_ware applica<on. •  Dockerfile: Set of instruc<ons/commands that are used to build the Docker image. •  CyVerse tools vs. apps: In the DE, a tool is an executable or binary upon which an app (an interface of a tool) is used to run the analyses.
6. 1. Install Docker hAps://docs.docker.com/docker-for-mac/ hAps://docs.docker.com/engine/installa<on/linux/ hAps://docs.docker.com/docker-for-windows/
7. 2. Planning Things to consider… •  What dependencies does your program have? •  Is the source code is already compiled? •  If not, how to compile your source code ? •  Best place to look is instruc<on manual •  hAp://www.bioinforma<cs.babraham.ac.uk/projects/fastqc/
8. 3. Create a Dockerfile, build and test Docker image FROM ubuntu:14.04.3 MAINTAINER Upendra Kumar DeviseAy <upendra@cyverse.org> LABEL Descrip<on="This image is used for crea<ng FastQC-0.11.5” RUN apt-get -y update RUN apt-get -y install wget unzip openjdk-7-jdk RUN wget hAp://www.bioinforma<cs.babraham.ac.uk/projects/fastqc/ fastqc_v0.11.5.zip \ && unzip fastqc_v0.11.5.zip \ && chmod +x FastQC/fastqc \ && cp -r FastQC/* /usr/bin ENTRYPOINT [ "fastqc" ]
9. 4. Tool request hAps://de.iplantcollabora<ve.org/de/
10. Your tool request for “fastqc“ has been completed. Before you can use your tool in the Discovery Environment, a user interface must be defined. You will find your tool listed in the Tool Editor under the name “fastqc“ and version “0.11.5“. 5. Wait to hear from us
11. 6. Design UI for your app and use it DEMO
12. •  Containers are very powerful and has many bells and whistles •  Avoid storing data inside of containers •  Keep containers light and nimble, build on provided base images from trusted source •  Do not trust a app without Dockerfile
13. The Process for Dockerizing tools in DE
14. The Process for Dockerizing tools in DE
15. Main Dockerfile commands •  FROM •  MAINTAINER •  LABEL •  RUN •  ENTRYPOINT •  WORKDIR •  ADD/COPY •  ENV •  EXPOSE